chr12-116761609-G-T

Position:

• chr12-116761609-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001382266.1(RNFT2):​c.628-5205G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0631 in 152,208 control chromosomes in the GnomAD database, including 825 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.063 (825 hom., cov: 32)
• Consequence: RNFT2 NM_001382266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

Genes affected

RNFT2 (HGNC:25905): (ring finger protein, transmembrane 2) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in positive regulation of ERAD pathway and protein ubiquitination. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNFT2	NM_001382266.1	c.628-5205G>T		intron_variant		ENST00000257575.9	NP_001369195.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNFT2	ENST00000257575.9	c.628-5205G>T		intron_variant		5	NM_001382266.1	ENSP00000257575	P1

Frequencies

GnomAD3 genomes AF: 0.0629 AC: 9571 AN: 152090 Hom.: 820 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0262

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00293

Gnomad OTH AF: 0.0507

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0631 AC: 9604 AN: 152208 Hom.: 825 Cov.: 32 AF XY: 0.0630 AC XY: 4686 AN XY: 74422

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0262

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.000282

Gnomad4 NFE AF: 0.00293

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0161 Hom.: 149

Bravo AF: 0.0693

Asia WGS AF: 0.123 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12322695; hg19: chr12-117199414;